Overview
This end-to-end automation pipeline eliminates the manual data entry bottleneck between raw synthesis outputs and the suite of enterprise R&D systems chemists rely on. A single data submission triggers a cascade of automated actions across four distinct platforms, ensuring data consistency and freeing chemists from repetitive administrative tasks.
The Problem
At the conclusion of each synthesis experiment, chemists typically need to manually:
- Register new compounds in the registration system
- Create synthesis and assay requests in the project tracker
- Write up a new experiment entry in the ELN
- Update campaign status reports for management
This repetitive multi-system data entry process is time-consuming, error-prone due to manual transcription, and often delayed — creating gaps in data traceability.
The Solution
Four-System Cascade Automation
A single submission of raw compound structure, synthesis reaction scheme, purification, and analytical method information triggers the following automated actions:
| Step | System | Action |
|---|---|---|
| 1 | CompReg | Compound registration with structure hash and metadata |
| 2 | Airtable | New synthesis & assay request records created |
| 3 | Signals ELN | New experiment entry populated with all relevant data |
| 4 | Dashboards | Weekly campaign status reports & BI dashboards generated |
Architecture
The system is built on a cronjob-based ETL process that:
- Pulls updates from an intermediate staging database
- Transforms data to each endpoint system’s required schema
- Pushes via each system’s respective REST API
The intermediate database acts as a single source of truth, ensuring all downstream systems remain synchronized even when individual API calls are retried.
Report Generation
Weekly campaign status reports are automatically generated per synthesis campaign, surfacing:
- Compound registration counts and success rates
- Assay request status and queue depth
- Synthesis yield and purity summaries
- Timeline tracking against campaign goals
Technical Stack
- Python for ETL orchestration
- Cron for scheduled execution
- REST APIs: CompReg, Airtable, Signals ELN
- PostgreSQL intermediate staging database
Impact
- Eliminated hours of manual data entry per synthesis campaign
- Ensured real-time data consistency across all R&D systems
- Reduced transcription errors to near-zero
- Provided management with automated, always-current campaign dashboards